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Use of locally weighted scatterplot smoothing ( LOWESS ) regression to study selection signatures in P iedmontese and I talian B rown cattle breeds
Author(s) -
Pintus Elia,
Sorbolini Silvia,
Albera Andrea,
Gaspa Giustino,
Dimauro Corrado,
Steri Roberto,
Marras Gabriele,
Macciotta Nicolò P. P.
Publication year - 2014
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12076
Subject(s) - biology , genetics , fixation index , population , selection (genetic algorithm) , quantitative trait locus , evolutionary biology , genetic variation , genetic structure , gene , demography , artificial intelligence , sociology , computer science
Summary Selection is the major force affecting local levels of genetic variation in species. The availability of dense marker maps offers new opportunities for a detailed understanding of genetic diversity distribution across the animal genome. Over the last 50 years, cattle breeds have been subjected to intense artificial selection. Consequently, regions controlling traits of economic importance are expected to exhibit selection signatures. The fixation index ( F st ) is an estimate of population differentiation, based on genetic polymorphism data, and it is calculated using the relationship between inbreeding and heterozygosity. In the present study, locally weighted scatterplot smoothing ( LOWESS ) regression and a control chart approach were used to investigate selection signatures in two cattle breeds with different production aptitudes (dairy and beef). F st was calculated for 42 514 SNP marker loci distributed across the genome in 749 Italian Brown and 364 Piedmontese bulls. The statistical significance of F st values was assessed using a control chart. The LOWESS technique was efficient in removing noise from the raw data and was able to highlight selection signatures in chromosomes known to harbour genes affecting dairy and beef traits. Examples include the peaks detected for BTA 2 in the region where the myostatin gene is located and for BTA 6 in the region harbouring the ABCG 2 locus. Moreover, several loci not previously reported in cattle studies were detected.